Woocommerce REST API: Add meta data to line-item and to the database

To save a metadata to a line_item (product that is in a order), you can hook the woocommerce_new_order_item action.

Hook it like this:

function my_line_item_metadata( $item_id, $item, $order_id ) {
   // Here you have the item, his id, and the order's id
   // You can get the order, for example
   $order = new WC_Order( $order_id );
   $items = $order->get_items();
   foreach( $items as $line_item_id => $item ) {
      // Here you can have all products from the order!
   }

      // Save here the metadata for the item id of the hooked line item
      wc_add_order_item_meta( $item_id, '_my_metadata', 'my metadata value' );
}
add_action( 'woocommerce_new_order_item', 'my_line_item_metadata', 10, 3 );

As you said that you using the WC API, you maybe want to add this field to the API return... to do it, use the following code:

/**
 * Add order meta to the REST API
 * @see http://codegists.com/code/order%20item%20meta%20rest%20response/
 *
 * @param \WP_REST_Response $response The response object.
 * @param \WP_Post $post Post object.
 * @param \WP_REST_Request $request Request object.
 * @return object updated response object
 */
function my_add_metadata_on_line_item( $response, $post, $request ) {

    $order_data = $response->get_data();

    foreach ( $order_data['line_items'] as $key => $item ) {
        $order_data['line_items'][ $key ]['_my_metadata'] = wc_get_order_item_meta( $item['id'], '_my_metadata', true );
    }

    $response->data = $order_data;

    return $response;
}
add_filter( 'woocommerce_rest_prepare_shop_order', 'my_add_metadata_on_line_item', 10, 3 );

Now your API will return the _my_metadata with the line item.

PS.: If you don't save your custom metadata with the _, WC will show the metadata in some places that you may not want to. With the _ the metadata will be hidden.